Research workbench
Crystal structure of the receptor binding domain of SARS-cov-2 spike glycoprotein in a ternary complex with covox-253 and covox-75 fabs
Analyse Crystal structure of the receptor binding domain of SARS-cov-2 spike… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BEN
- Type
- protein
- Length
- 2,095 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Covox-253 heavy chain; Covox-253 light chain; Covox-75 heavy chain…
- UniProt
- P0DTC2
- Ligands
- NAG, FUC, BR, IOD
- Pockets
- 20 · best druggability 0.67
Structure
x-ray diffraction · 6 distinct chains · 10% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Spike glycoprotein | protein | 177 | 15% helix, 27% strand | P0DTC2 |
| H, D | Covox-253 heavy chain | protein | 219 | 9% helix, 51% strand | — |
| L, F | Covox-253 light chain | protein | 214 | 7% helix, 52% strand | — |
| A, G | Covox-75 heavy chain | protein | 224 | 9% helix, 51% strand | — |
| B, I | Covox-75 light chain | protein | 213 | 5% helix, 51% strand | — |
| C | Spike glycoprotein | protein | 178 | 15% helix, 29% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains H, D, C
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains H, D
- BR · Bromide ion · ion · 14 copies · chains H, L, A, B, E, D, F, G, I, C
- IOD · Iodide ion · ion · chains G, I
- GOL · Glycerol · additive · 5 copies · chains E, L, A, B, C, F
- IMD · Imidazole · additive · 4 copies · chains E, A, B, F, I
- PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · 2 copies · chains H, L, D, F
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 710 | 0.67 | 0.75 | 77 | BR |
| 2 | 689 | 0.65 | 0.75 | 71 | BR |
| 3 | 522 | 0.62 | 0.75 | 54 | PG6 |
| 4 | 162 | 0.62 | 0.84 | 34 | empty |
| 5 | 486 | 0.60 | 0.75 | 57 | PG6 |
Interfaces
16 interfaces between chains.
- D–F · 1749 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 1728 Ų buried · 15 hydrogen bonds · protein-protein
- G–I · 1711 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1709 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 604 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7BEN · Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a… · the same entry in another collection · chain E against E, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7BEN · PDBe 7BEN · UniProt P0DTC2
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